Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Use docker profile run test data error #14

Open
flowhub-team opened this issue Aug 4, 2023 · 1 comment
Open

Use docker profile run test data error #14

flowhub-team opened this issue Aug 4, 2023 · 1 comment
Labels
bug Something isn't working

Comments

@flowhub-team
Copy link

Description of the bug

When I run the Docker profile using virtoprofiler, I run test data with the command/ Nextflow run deng lab/viroprofiler - r main - profile docker, test, but an error was reported.

Command used and terminal output

./nextflow run deng-lab/viroprofiler -r main -profile docker,test


-[ViroProfiler] Pipeline completed with errors-
ERROR ~ Error executing process > 'VIROPROFILER:CHECKV'

Caused by:
  Process `VIROPROFILER:CHECKV` terminated with an error exit status (1)

Command executed:

  run_checkv.sh contigs_cclib_long.fasta.gz 3000 $(pwd) 1 spades /root/viroprofiler/checkv
  mv viruses.fna checkv_qc.fasta
  while [ -s proviruses_nextInput.fna ] ; do
      dir_new=run_$(date +"%Y%m%d%h%s")
      run_checkv.sh proviruses_nextInput.fna 3000 $dir_new 1 spades /root/viroprofiler/checkv
      cat $dir_new/viruses.fna >> checkv_qc.fasta
      csvtk concat -t quality_summary_viruses.tsv $dir_new/quality_summary_viruses.tsv > quality_summary.tsv
      cp quality_summary.tsv quality_summary_viruses.tsv
      sed 1d $dir_new/quality_summary_proviruses.tsv >> quality_summary_proviruses.tsv
      cat $dir_new/proviruses_short.fna >> proviruses_short.fna
      cat $dir_new/proviruse_ids_raw.list >> proviruse_ids_raw.list
      cat $dir_new/proviruse_ids_clean.list >> proviruse_ids_clean.list
      cp $dir_new/proviruses_nextInput.fna .
      sleep 1
  done
  seqkit seq -m 3000 checkv_qc.fasta > checkv_qc_long.fasta

  cat <<-END_VERSIONS > versions.yml
  "VIROPROFILER:CHECKV":
      CheckV: $(echo $(checkv | head -n1 | sed 's/:.*//' | sed 's/CheckV v//'))
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:

  CheckV v1.0.1: contamination
  [1/8] Reading database info...
  [2/8] Reading genome info...
  [3/8] Calling genes with Prodigal...
  [4/8] Reading gene info...
  [5/8] Running hmmsearch...
  [6/8] Annotating genes...
  [7/8] Identifying host regions...
  [8/8] Writing results...
  Run time: 73.23 seconds
  Peak mem: 0.24 GB

  CheckV v1.0.1: completeness
  [1/8] Skipping gene calling...
  [2/8] Initializing queries and database...
  [3/8] Running DIAMOND blastp search...
  [4/8] Computing AAI...
  [5/8] Running AAI based completeness estimation...
  [6/8] Running HMM based completeness estimation...
  [7/8] Determining genome copy number...
  [8/8] Writing results...
  Run time: 23.19 seconds
  Peak mem: 1.92 GB

  CheckV v1.0.1: complete_genomes
  [1/7] Reading input sequences...
  [2/7] Finding complete proviruses...
  [3/7] Finding direct/inverted terminal repeats...
  [4/7] Filtering terminal repeats...
  [5/7] Checking genome for completeness...
  [6/7] Checking genome for large duplications...
  [7/7] Writing results...
  Run time: 0.02 seconds
  Peak mem: 1.92 GB

  CheckV v1.0.1: quality_summary
  [1/6] Reading input sequences...
  [2/6] Reading results from contamination module...
  [3/6] Reading results from completeness module...
  [4/6] Reading results from complete genomes module...
  [5/6] Classifying contigs into quality tiers...
  [6/6] Writing results...
  Run time: 0.01 seconds
  Peak mem: 1.92 GB
  Traceback (most recent call last):
    File "/root/.nextflow/assets/deng-lab/viroprofiler/bin/correct_spades_contig_length.py", line 5, in <module>
      from Bio import SeqIO
  ModuleNotFoundError: No module named 'Bio'

Work dir:
  /root/work/ec/257e6e3b81260568daf2a6d5051fb4

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details

Relevant files

Aug-04 09:56:56.412 [main] DEBUG nextflow.cli.Launcher - $> nextflow run deng-lab/viroprofiler -r main -profile docker,test
Aug-04 09:56:56.476 [main] INFO nextflow.cli.CmdRun - N E X T F L O W ~ version 23.04.2
Aug-04 09:56:56.492 [main] DEBUG nextflow.plugin.PluginsFacade - Setting up plugin manager > mode=prod; embedded=false; plugins-dir=/root/.nextflow/plugins; core-plugins: [email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected],[email protected]
Aug-04 09:56:56.499 [main] INFO org.pf4j.DefaultPluginStatusProvider - Enabled plugins: []
Aug-04 09:56:56.500 [main] INFO org.pf4j.DefaultPluginStatusProvider - Disabled plugins: []
Aug-04 09:56:56.503 [main] INFO org.pf4j.DefaultPluginManager - PF4J version 3.4.1 in 'deployment' mode
Aug-04 09:56:56.510 [main] INFO org.pf4j.AbstractPluginManager - No plugins
Aug-04 09:56:56.521 [main] DEBUG nextflow.scm.ProviderConfig - Using SCM config path: /root/.nextflow/scm
Aug-04 09:56:57.689 [main] DEBUG nextflow.scm.AssetManager - Git config: /root/.nextflow/assets/deng-lab/viroprofiler/.git/config; branch: master; remote: origin; url: https://github.com/deng-lab/viroprofiler.git
Aug-04 09:56:57.707 [main] DEBUG nextflow.scm.RepositoryFactory - Found Git repository result: [RepositoryFactory]
Aug-04 09:56:57.714 [main] DEBUG nextflow.scm.AssetManager - Git config: /root/.nextflow/assets/deng-lab/viroprofiler/.git/config; branch: master; remote: origin; url: https://github.com/deng-lab/viroprofiler.git
Aug-04 09:56:58.739 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /root/.nextflow/assets/deng-lab/viroprofiler/nextflow.config
Aug-04 09:56:58.740 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /root/.nextflow/assets/deng-lab/viroprofiler/nextflow.config
Aug-04 09:56:58.746 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: docker,test
Aug-04 09:56:59.441 [main] DEBUG nextflow.config.ConfigBuilder - Available config profiles: [standard, debug, test, apptainer, docker, shifter, charliecloud, test_denglab, conda, singularity, charliecloud_denglab, podman, slurm_denglab2]
Aug-04 09:56:59.466 [main] DEBUG nextflow.cli.CmdRun - Applied DSL=2 from script declararion
Aug-04 09:56:59.466 [main] INFO nextflow.cli.CmdRun - Launching https://github.com/deng-lab/viroprofiler [big_wozniak] DSL2 - revision: c2a1f18 [main]
Aug-04 09:56:59.467 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins default=[]
Aug-04 09:56:59.467 [main] DEBUG nextflow.plugin.PluginsFacade - Plugins resolved requirement=[]
Aug-04 09:56:59.469 [main] DEBUG nextflow.secret.LocalSecretsProvider - Secrets store: /root/.nextflow/secrets/store.json
Aug-04 09:56:59.471 [main] DEBUG nextflow.secret.SecretsLoader - Discovered secrets providers: [nextflow.secret.LocalSecretsProvider@240a2619] - activable => nextflow.secret.LocalSecretsProvider@240a2619
Aug-04 09:56:59.512 [main] DEBUG nextflow.Session - Session UUID: 8366e9d9-2a58-4580-9412-d6b9ec23aa9c
Aug-04 09:56:59.512 [main] DEBUG nextflow.Session - Run name: big_wozniak
Aug-04 09:56:59.513 [main] DEBUG nextflow.Session - Executor pool size: 8
Aug-04 09:56:59.521 [main] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'FileTransfer' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
Aug-04 09:56:59.535 [main] DEBUG nextflow.cli.CmdRun -
Version: 23.04.2 build 5870
Created: 08-06-2023 08:29 UTC (16:29 CDT)
System: Linux 5.15.0-73-generic
Runtime: Groovy 3.0.16 on OpenJDK 64-Bit Server VM 17.0.8+7-Ubuntu-122.04
Encoding: UTF-8 (UTF-8)
Process: 43715@iZj6c6klemvicp1e0upziuZ [172.24.234.30]
CPUs: 8 - Mem: 14.7 GB (8.4 GB) - Swap: 0 (0)
Aug-04 09:56:59.545 [main] DEBUG nextflow.Session - Work-dir: /root/work [ext2/ext3]
Aug-04 09:56:59.557 [main] DEBUG nextflow.executor.ExecutorFactory - Extension executors providers=[]
Aug-04 09:56:59.563 [main] DEBUG nextflow.Session - Observer factory: DefaultObserverFactory
Aug-04 09:56:59.661 [main] DEBUG nextflow.cache.CacheFactory - Using Nextflow cache factory: nextflow.cache.DefaultCacheFactory
Aug-04 09:56:59.668 [main] DEBUG nextflow.util.CustomThreadPool - Creating default thread pool > poolSize: 9; maxThreads: 1000
Aug-04 09:56:59.717 [main] DEBUG nextflow.Session - Session start
Aug-04 09:56:59.721 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow started -- trace file: /root/output/pipeline_info/execution_trace_2023-08-04_09-56-59.txt
Aug-04 09:56:59.727 [main] DEBUG nextflow.Session - Using default localLib path: /root/.nextflow/assets/deng-lab/viroprofiler/lib
Aug-04 09:56:59.729 [main] DEBUG nextflow.Session - Adding to the classpath library: /root/.nextflow/assets/deng-lab/viroprofiler/lib
Aug-04 09:56:59.729 [main] DEBUG nextflow.Session - Adding to the classpath library: /root/.nextflow/assets/deng-lab/viroprofiler/lib/nfcore_external_java_deps.jar
Aug-04 09:57:00.498 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
Aug-04 09:57:00.628 [main] INFO nextflow.Nextflow -

-�[2m--------------------------------------------------------------------------------------------------------------�[0m-
�[0;34m __ �[0m
�[0;34m oooooo oooo o8o 88 88 .o88o. o8o oooo �[0m
�[0;34m 888. .8' "' 88 ss 88 888 " "' 888 �[0m �[0;34m 888. .8' oooo oooo d8b .ooooo. 88__88 oooo d8b .ooooo. o888oo oooo 888 .ooooo. oooo d8b �[0m
�[0;34m 888. .8' 888 888""8P d88' 88b || 888""8P d88' 88b 888 888 888 d88' 88b 888""8P �[0m �[0;34m 888.8' 888 888 888 888 || 888 888 888 888 888 888 888ooo888 888 �[0m
�[0;34m 888' 888 888 888 888 // || \\ 888 888 888 888 888 888 888 .o 888 �[0m �[0;34m 8' o888o d888b Y8bod8P' // \\ d888b Y8bod8P' o888o o888o o888o `Y8bod8P' d888b �[0m
�[0;35m ViroProfiler v0.2.4�[0m
-�[2m--------------------------------------------------------------------------------------------------------------�[0m-
�[1mCore Nextflow options�[0m
�[0;34mrevision : �[0;32mmain�[0m
�[0;34mrunName : �[0;32mbig_wozniak�[0m
�[0;34mcontainerEngine : �[0;32mdocker�[0m
�[0;34mlaunchDir : �[0;32m/root�[0m
�[0;34mworkDir : �[0;32m/root/work�[0m
�[0;34mprojectDir : �[0;32m/root/.nextflow/assets/deng-lab/viroprofiler�[0m
�[0;34muserName : �[0;32mroot�[0m
�[0;34mprofile : �[0;32mdocker,test�[0m
�[0;34mconfigFiles : �[0;32m/root/.nextflow/assets/deng-lab/viroprofiler/nextflow.config�[0m

�[1mInput/output options�[0m
�[0;34mmode : �[0;32mall�[0m
�[0;34minput : �[0;32mhttps://raw.githubusercontent.com/deng-lab/viroprofiler/main/assets/samplesheet.csv�[0m
�[0;34mdb : �[0;32m/root/viroprofiler�[0m
�[0;34moutdir : �[0;32moutput�[0m

�[1mQC�[0m
�[0;34mcontamref_idx : �[0;32m/root/viroprofiler/contamination_refs/hg19/ref�[0m

�[1mContig library parameters�[0m
�[0;34massemblies : �[0;32mscaffolds�[0m

�[1mOthers�[0m
�[0;34muse_iphop : �[0;32mtrue�[0m
�[0;34muse_dram : �[0;32mtrue�[0m

�[1mInstitutional config options�[0m
�[0;34mconfig_profile_name : �[0;32mTest profile�[0m
�[0;34mconfig_profile_description: �[0;32mMinimal test dataset to check pipeline function�[0m

�[1mMax job request options�[0m
�[0;34mmax_cpus : �[0;32m2�[0m
�[0;34mmax_memory : �[0;32m6.GB�[0m
�[0;34mmax_time : �[0;32m24.h�[0m

!! Only displaying parameters that differ from the pipeline defaults !!
-�[2m--------------------------------------------------------------------------------------------------------------�[0m-
If you use ViroProfiler for your analysis please cite:

  • The ViroProfiler pipeline
    Ru, Jinlong, et al. "ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis."
    Gut Microbes 15.1 (2023): 2192522. https://doi.org/10.1080/19490976.2023.2192522

  • The nf-core framework
    Ewels, Philip A., et al. "The nf-core framework for community-curated bioinformatics pipelines."
    Nature biotechnology 38.3 (2020): 276-278. https://doi.org/10.1038/s41587-020-0439-x

  • Software dependencies
    https://github.com/deng-lab/viroprofiler/blob/main/CITATIONS.md
    -�[2m--------------------------------------------------------------------------------------------------------------�[0m-
    Aug-04 09:57:02.623 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name VIROPROFILER:FASTQC
    Aug-04 09:57:02.625 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:FASTQC matches process VIROPROFILER:FASTQC
    Aug-04 09:57:02.629 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.629 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.634 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
    Aug-04 09:57:02.637 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=8; memory=14.7 GB; capacity=8; pollInterval=100ms; dumpInterval=5m
    Aug-04 09:57:02.688 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name VIROPROFILER:FASTP
    Aug-04 09:57:02.689 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:FASTP matches process VIROPROFILER:FASTP
    Aug-04 09:57:02.691 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.691 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.709 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_high matches labels process_high for process with name VIROPROFILER:SPADES
    Aug-04 09:57:02.710 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:SPADES matches process VIROPROFILER:SPADES
    Aug-04 09:57:02.711 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.711 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.716 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_base matches labels viroprofiler_base for process with name VIROPROFILER:CONTIGLIB
    Aug-04 09:57:02.717 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:CONTIGLIB matches process VIROPROFILER:CONTIGLIB
    Aug-04 09:57:02.718 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.718 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.722 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_base matches labels viroprofiler_base for process with name VIROPROFILER:CHECKV
    Aug-04 09:57:02.722 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:CHECKV matches process VIROPROFILER:CHECKV
    Aug-04 09:57:02.723 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.723 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.726 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_base matches labels viroprofiler_base for process with name VIROPROFILER:CONTIGLIB_CLUSTER
    Aug-04 09:57:02.726 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:CONTIGLIB_CLUSTER matches process VIROPROFILER:CONTIGLIB_CLUSTER
    Aug-04 09:57:02.727 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.727 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.731 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_base matches labels viroprofiler_base for process with name VIROPROFILER:GENEPRED4CTG
    Aug-04 09:57:02.731 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:GENEPRED matches process VIROPROFILER:GENEPRED4CTG
    Aug-04 09:57:02.732 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.732 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.736 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_geneannot matches labels viroprofiler_geneannot for process with name VIROPROFILER:NRPROT
    Aug-04 09:57:02.737 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:NRSEQS matches process VIROPROFILER:NRPROT
    Aug-04 09:57:02.738 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.738 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.741 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_geneannot matches labels viroprofiler_geneannot for process with name VIROPROFILER:NRGENE
    Aug-04 09:57:02.741 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:NRSEQS matches process VIROPROFILER:NRGENE
    Aug-04 09:57:02.743 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.743 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.747 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_abundance matches labels viroprofiler_abundance for process with name VIROPROFILER:CONTIGINDEX
    Aug-04 09:57:02.748 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.748 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.751 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_abundance matches labels viroprofiler_abundance for process with name VIROPROFILER:MAPPING2CONTIGS2
    Aug-04 09:57:02.752 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.752 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.756 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_base matches labels viroprofiler_base for process with name VIROPROFILER:ABUNDANCE
    Aug-04 09:57:02.756 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:ABUNDANCE matches process VIROPROFILER:ABUNDANCE
    Aug-04 09:57:02.757 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.757 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.760 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_vibrant matches labels viroprofiler_vibrant for process with name VIROPROFILER:VIBRANT
    Aug-04 09:57:02.760 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:VIBRANT matches process VIROPROFILER:VIBRANT
    Aug-04 09:57:02.761 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.761 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.763 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_binning matches labels viroprofiler_binning for process with name VIROPROFILER:DVF
    Aug-04 09:57:02.763 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:DVF matches process VIROPROFILER:DVF
    Aug-04 09:57:02.764 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.764 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.767 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_base matches labels viroprofiler_base for process with name VIROPROFILER:VIRCONTIGS_PRE
    Aug-04 09:57:02.768 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.768 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.771 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_virsorter2 matches labels viroprofiler_virsorter2 for process with name VIROPROFILER:VIRSORTER2
    Aug-04 09:57:02.772 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:VIRSORTER2 matches process VIROPROFILER:VIRSORTER2
    Aug-04 09:57:02.773 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.773 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.778 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_geneannot matches labels viroprofiler_geneannot for process with name VIROPROFILER:DRAMV
    Aug-04 09:57:02.778 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:DRAMV matches process VIROPROFILER:DRAMV
    Aug-04 09:57:02.779 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.779 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.782 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_taxa matches labels viroprofiler_taxa for process with name VIROPROFILER:TAXONOMY_VCONTACT
    Aug-04 09:57:02.782 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:TAXONOMY_VCONTACT matches process VIROPROFILER:TAXONOMY_VCONTACT
    Aug-04 09:57:02.783 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.783 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.785 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_base matches labels viroprofiler_base for process with name VIROPROFILER:TAXONOMY_MMSEQS
    Aug-04 09:57:02.785 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:TAXONOMY_MMSEQS matches process VIROPROFILER:TAXONOMY_MMSEQS
    Aug-04 09:57:02.786 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.786 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.788 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_taxa matches labels viroprofiler_taxa for process with name VIROPROFILER:TAXONOMY_MERGE
    Aug-04 09:57:02.789 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:TAXONOMY_MERGE matches process VIROPROFILER:TAXONOMY_MERGE
    Aug-04 09:57:02.789 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.790 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.792 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_host matches labels viroprofiler_host for process with name VIROPROFILER:VIRALHOST_IPHOP
    Aug-04 09:57:02.792 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:VIRALHOST_IPHOP matches process VIROPROFILER:VIRALHOST_IPHOP
    Aug-04 09:57:02.793 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.793 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.798 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_replicyc matches labels viroprofiler_replicyc for process with name VIROPROFILER:BACPHLIP
    Aug-04 09:57:02.798 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:BACPHLIP matches process VIROPROFILER:BACPHLIP
    Aug-04 09:57:02.799 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.799 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.803 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:viroprofiler_vpfkit matches labels viroprofiler_vpfkit for process with name VIROPROFILER:RESULTS_TSE
    Aug-04 09:57:02.804 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.804 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.823 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_low matches labels process_low for process with name VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS
    Aug-04 09:57:02.823 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:CUSTOM_DUMPSOFTWAREVERSIONS matches process VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS
    Aug-04 09:57:02.824 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.824 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.833 [main] DEBUG nextflow.script.ProcessConfig - Config settings withLabel:process_medium matches labels process_medium for process with name VIROPROFILER:MULTIQC
    Aug-04 09:57:02.833 [main] DEBUG nextflow.script.ProcessConfig - Config settings withName:MULTIQC matches process VIROPROFILER:MULTIQC
    Aug-04 09:57:02.834 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
    Aug-04 09:57:02.834 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
    Aug-04 09:57:02.839 [main] DEBUG nextflow.Session - Workflow process names [dsl2]: VIROPROFILER:ABUNDANCE, DB_VOGDB, GENEPRED4BIN, CHECKV, VIRSORTER2, VIROPROFILER:CONTIGLIB_CLUSTER, DB_VIBRANT, VIROPROFILER:VIRSORTER2, FASTP, VIROPROFILER:DVF, VIROPROFILER:TAXONOMY_MMSEQS, VIROPROFILER:VIRALHOST_IPHOP, BBMAP_ALIGN, ABUNDANCE, PHAMB_RF, MAPPING2CONTIGS2, GENEPRED4CTG, VIBRANT, CONTIGLIB, VIROPROFILER:CONTIGLIB, VIROPROFILER:FASTQC, VIROPROFILER:RESULTS_TSE, VIROPROFILER:SPADES, VAMB, VIROPROFILER:BACPHLIP, VIROPROFILER:DRAMV, BRACKEN_COMBINEBRACKENOUTPUTS, VIROPROFILER:MULTIQC, DB_VIRSORTER2, DECONTAM, VIRALHOST_IPHOP, DRAMV, DB_KRAKEN2, VIROPROFILER:NRGENE, GENEPRED, CONTIGLIB_CLUSTER, DB_VIROPROFILER, FASTQC, VIROPROFILER:GENEPRED4CTG, CHECKV4PHAMB, VRHYME, VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS, TAXONOMY_MERGE, SPADES, VIROPROFILER:CONTIGINDEX, VIROPROFILER:NRPROT, MULTIQC, VIROPROFILER:VIRCONTIGS_PRE, VOGDB, VIROPROFILER:TAXONOMY_VCONTACT, DB_PHAMB, DB_IPHOP, VIROPROFILER:TAXONOMY_MERGE, CHECKV4VRHYME, RESULTS_TSE, DB_MICOMPLETEDB, TAXONOMY_VCONTACT, TAXONOMY_MMSEQS, DB_CHECKV, CONTIGINDEX, MICOMPLETEDB, VIROPROFILER:CHECKV, NRGENE, DB_VREFSEQ, NRPROT, EMAPPER, VIROPROFILER:MAPPING2CONTIGS2, MAPPING2CONTIGS, REPLIDEC, BRACKEN_DB, DB_EGGNOG, VIROPROFILER:FASTP, DVF, VIROPROFILER:VIBRANT, BACPHLIP, DB_DRAM, CUSTOM_DUMPSOFTWAREVERSIONS, VIRCONTIGS_PRE, NRSEQS, ABRICATE, BRACKEN
    Aug-04 09:57:02.844 [main] DEBUG nextflow.Session - Igniting dataflow network (31)
    Aug-04 09:57:02.845 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:FASTQC
    Aug-04 09:57:02.845 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:FASTP
    Aug-04 09:57:02.845 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:SPADES
    Aug-04 09:57:02.846 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:CONTIGLIB
    Aug-04 09:57:02.846 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:CHECKV
    Aug-04 09:57:02.846 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:CONTIGLIB_CLUSTER
    Aug-04 09:57:02.846 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:GENEPRED4CTG
    Aug-04 09:57:02.846 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:NRPROT
    Aug-04 09:57:02.846 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:NRGENE
    Aug-04 09:57:02.846 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:CONTIGINDEX
    Aug-04 09:57:02.846 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:MAPPING2CONTIGS2
    Aug-04 09:57:02.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:ABUNDANCE
    Aug-04 09:57:02.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:VIBRANT
    Aug-04 09:57:02.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:DVF
    Aug-04 09:57:02.847 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:VIRCONTIGS_PRE
    Aug-04 09:57:02.848 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:VIRSORTER2
    Aug-04 09:57:02.848 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:DRAMV
    Aug-04 09:57:02.848 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:TAXONOMY_VCONTACT
    Aug-04 09:57:02.848 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:TAXONOMY_MMSEQS
    Aug-04 09:57:02.848 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:TAXONOMY_MERGE
    Aug-04 09:57:02.848 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:VIRALHOST_IPHOP
    Aug-04 09:57:02.848 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:BACPHLIP
    Aug-04 09:57:02.848 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:RESULTS_TSE
    Aug-04 09:57:02.848 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:CUSTOM_DUMPSOFTWAREVERSIONS
    Aug-04 09:57:02.848 [main] DEBUG nextflow.processor.TaskProcessor - Starting process > VIROPROFILER:MULTIQC
    Aug-04 09:57:02.848 [main] DEBUG nextflow.script.ScriptRunner - > Awaiting termination
    Aug-04 09:57:02.848 [main] DEBUG nextflow.Session - Session await
    Aug-04 09:57:02.933 [Actor Thread 10] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 1; slices: 1; internal sort time: 0.0 s; external sort time: 0.01 s; total time: 0.01 s
    Aug-04 09:57:02.938 [Actor Thread 10] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /root/work/collect-file/5b304b93ca49088ffe32cffb120fddd7
    Aug-04 09:57:02.943 [Actor Thread 10] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-3383267904818912750
    Aug-04 09:57:04.207 [FileTransfer-1] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/rujinlong/test/main/data/HT02_R1.fq.gz to work dir: /root/work/stage-8366e9d9-2a58-4580-9412-d6b9ec23aa9c/58/9ea8c46407799372d07fa536e1d2d6/HT02_R1.fq.gz
    Aug-04 09:57:04.207 [FileTransfer-2] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/rujinlong/test/main/data/HT02_R2.fq.gz to work dir: /root/work/stage-8366e9d9-2a58-4580-9412-d6b9ec23aa9c/de/6df08e9f304dc7b61e204f6e20f522/HT02_R2.fq.gz
    Aug-04 09:57:04.361 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:57:04.363 [Task submitter] INFO nextflow.Session - [ef/055d50] Submitted process > VIROPROFILER:FASTQC (HT02)
    Aug-04 09:57:04.373 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:57:04.374 [Task submitter] INFO nextflow.Session - [c1/2e4e05] Submitted process > VIROPROFILER:FASTP (HT02)
    Aug-04 09:57:04.890 [FileTransfer-3] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/rujinlong/test/main/data/HT04_R1.fq.gz to work dir: /root/work/stage-8366e9d9-2a58-4580-9412-d6b9ec23aa9c/66/b3052ed3227daf6c33e1d8416b462b/HT04_R1.fq.gz
    Aug-04 09:57:04.890 [FileTransfer-4] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/rujinlong/test/main/data/HT04_R2.fq.gz to work dir: /root/work/stage-8366e9d9-2a58-4580-9412-d6b9ec23aa9c/a7/1d004e73375773f6005da6f6e6e38f/HT04_R2.fq.gz
    Aug-04 09:57:05.031 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:57:05.032 [Task submitter] INFO nextflow.Session - [f4/062b15] Submitted process > VIROPROFILER:FASTQC (HT04)
    Aug-04 09:57:05.037 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:57:05.038 [Task submitter] INFO nextflow.Session - [a3/dd973b] Submitted process > VIROPROFILER:FASTP (HT04)
    Aug-04 09:57:05.744 [FileTransfer-6] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/rujinlong/test/main/data/UC20_R2.fq.gz to work dir: /root/work/stage-8366e9d9-2a58-4580-9412-d6b9ec23aa9c/65/f1c9bf7802e884add124162f2b2709/UC20_R2.fq.gz
    Aug-04 09:57:05.746 [FileTransfer-5] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/rujinlong/test/main/data/UC20_R1.fq.gz to work dir: /root/work/stage-8366e9d9-2a58-4580-9412-d6b9ec23aa9c/fd/84a247465bcd78bce5cd4d41fb8d6e/UC20_R1.fq.gz
    Aug-04 09:57:05.922 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:57:05.926 [Task submitter] INFO nextflow.Session - [ce/00f5f6] Submitted process > VIROPROFILER:FASTQC (UC20)
    Aug-04 09:57:05.930 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:57:05.934 [Task submitter] INFO nextflow.Session - [10/6afe86] Submitted process > VIROPROFILER:FASTP (UC20)
    Aug-04 09:57:06.296 [FileTransfer-8] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/rujinlong/test/main/data/UC21_R2.fq.gz to work dir: /root/work/stage-8366e9d9-2a58-4580-9412-d6b9ec23aa9c/f7/5b74b0bdd7b17e440016594f047cd3/UC21_R2.fq.gz
    Aug-04 09:57:06.299 [FileTransfer-7] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/rujinlong/test/main/data/UC21_R1.fq.gz to work dir: /root/work/stage-8366e9d9-2a58-4580-9412-d6b9ec23aa9c/90/57d9d982a8881ec9855d6d319671fc/UC21_R1.fq.gz
    Aug-04 09:57:06.398 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:57:06.399 [Task submitter] INFO nextflow.Session - [4e/b7b5f8] Submitted process > VIROPROFILER:FASTQC (UC21)
    Aug-04 09:57:06.963 [FileTransfer-9] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/rujinlong/test/main/data/UC24_R1.fq.gz to work dir: /root/work/stage-8366e9d9-2a58-4580-9412-d6b9ec23aa9c/df/5bd6642b981d90ea5a006912fe5d95/UC24_R1.fq.gz
    Aug-04 09:57:06.970 [FileTransfer-10] DEBUG nextflow.file.FilePorter - Copying foreign file https://raw.githubusercontent.com/rujinlong/test/main/data/UC24_R2.fq.gz to work dir: /root/work/stage-8366e9d9-2a58-4580-9412-d6b9ec23aa9c/1b/68f319c1e0b2965a33f9514ff5f22f/UC24_R2.fq.gz
    Aug-04 09:57:11.927 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: VIROPROFILER:FASTQC (HT02); status: COMPLETED; exit: 0; error: -; workDir: /root/work/ef/055d506e021bd46706a1318536f97a]
    Aug-04 09:57:11.932 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:57:11.933 [Task submitter] INFO nextflow.Session - [88/2d462e] Submitted process > VIROPROFILER:FASTP (UC21)
    Aug-04 09:57:11.955 [Task monitor] DEBUG nextflow.util.ThreadPoolBuilder - Creating thread pool 'PublishDir' minSize=10; maxSize=24; workQueue=LinkedBlockingQueue[10000]; allowCoreThreadTimeout=false
    Aug-04 09:57:12.394 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: VIROPROFILER:FASTP (HT02); status: COMPLETED; exit: 0; error: -; workDir: /root/work/c1/2e4e05a65332f594f23f6d5992363a]
    Aug-04 09:57:12.398 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:57:12.398 [Task submitter] INFO nextflow.Session - [9c/5d23c3] Submitted process > VIROPROFILER:FASTP (UC24)
    Aug-04 09:57:12.519 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
    Aug-04 09:57:12.519 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
    Aug-04 09:57:12.538 [Actor Thread 5] DEBUG nextflow.util.CacheHelper - [WARN] Unknown hashing type: class nextflow.util.MemoryUnit
    Aug-04 09:57:13.371 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 3; name: VIROPROFILER:FASTQC (HT04); status: COMPLETED; exit: 0; error: -; workDir: /root/work/f4/062b15323d14efe32a9a5762b7e840]
    Aug-04 09:57:13.377 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:57:13.377 [Task submitter] INFO nextflow.Session - [71/d7e6c8] Submitted process > VIROPROFILER:FASTQC (UC24)
    Aug-04 09:57:14.017 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 8; name: VIROPROFILER:FASTQC (UC21); status: COMPLETED; exit: 0; error: -; workDir: /root/work/4e/b7b5f8669e41bf93d0ec7c891db799]
    Aug-04 09:57:14.279 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 5; name: VIROPROFILER:FASTQC (UC20); status: COMPLETED; exit: 0; error: -; workDir: /root/work/ce/00f5f6fc87f2ebc861a8c9feedb246]
    Aug-04 09:57:19.415 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 9; name: VIROPROFILER:FASTQC (UC24); status: COMPLETED; exit: 0; error: -; workDir: /root/work/71/d7e6c82b186d48f35b8ae1b01d265a]
    Aug-04 09:57:19.418 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:57:19.419 [Task submitter] INFO nextflow.Session - [55/d687ea] Submitted process > VIROPROFILER:SPADES (HT02)
    Aug-04 09:57:19.967 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 4; name: VIROPROFILER:FASTP (HT04); status: COMPLETED; exit: 0; error: -; workDir: /root/work/a3/dd973b3ce99150d481bfcc62d7fe3d]
    Aug-04 09:57:19.972 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
    Aug-04 09:57:19.972 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
    Aug-04 09:57:20.212 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: VIROPROFILER:FASTP (UC21); status: COMPLETED; exit: 0; error: -; workDir: /root/work/88/2d462e336af57b01e4d2d99fb4d09a]
    Aug-04 09:57:20.218 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
    Aug-04 09:57:20.219 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
    Aug-04 09:57:20.253 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 6; name: VIROPROFILER:FASTP (UC20); status: COMPLETED; exit: 0; error: -; workDir: /root/work/10/6afe86fd2ef41d78634a5c942be717]
    Aug-04 09:57:20.257 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:57:20.258 [Task submitter] INFO nextflow.Session - [6b/6145fd] Submitted process > VIROPROFILER:SPADES (HT04)
    Aug-04 09:57:20.263 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
    Aug-04 09:57:20.263 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
    Aug-04 09:57:23.572 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 10; name: VIROPROFILER:FASTP (UC24); status: COMPLETED; exit: 0; error: -; workDir: /root/work/9c/5d23c317901491863184320f83a7b9]
    Aug-04 09:57:23.576 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<5:1>
    Aug-04 09:57:23.576 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:FASTP > Skipping output binding because one or more optional files are missing: fileoutparam<6:1>
    Aug-04 09:57:25.979 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 11; name: VIROPROFILER:SPADES (HT02); status: COMPLETED; exit: 0; error: -; workDir: /root/work/55/d687eaf7bd95cf56e4e94bb289aa9e]
    Aug-04 09:57:25.981 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:57:25.982 [Task submitter] INFO nextflow.Session - [1f/b3046b] Submitted process > VIROPROFILER:SPADES (UC21)
    Aug-04 09:57:25.984 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:SPADES > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
    Aug-04 09:57:25.984 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:SPADES > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
    Aug-04 09:57:33.899 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 13; name: VIROPROFILER:SPADES (UC21); status: COMPLETED; exit: 0; error: -; workDir: /root/work/1f/b3046bb144f68cbf6aea9d4183342e]
    Aug-04 09:57:33.902 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:57:33.902 [Task submitter] INFO nextflow.Session - [97/33a164] Submitted process > VIROPROFILER:SPADES (UC20)
    Aug-04 09:57:33.903 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:SPADES > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
    Aug-04 09:57:33.903 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:SPADES > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
    Aug-04 09:57:40.854 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 12; name: VIROPROFILER:SPADES (HT04); status: COMPLETED; exit: 0; error: -; workDir: /root/work/6b/6145fd7d33a88a4bdfb82d241a8160]
    Aug-04 09:57:40.857 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:57:40.857 [Task submitter] INFO nextflow.Session - [34/ffc86c] Submitted process > VIROPROFILER:SPADES (UC24)
    Aug-04 09:57:40.859 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:SPADES > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
    Aug-04 09:57:40.859 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:SPADES > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
    Aug-04 09:57:52.104 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 15; name: VIROPROFILER:SPADES (UC24); status: COMPLETED; exit: 0; error: -; workDir: /root/work/34/ffc86cdd910755dff24e175e84fc56]
    Aug-04 09:57:52.108 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:SPADES > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
    Aug-04 09:57:52.108 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:SPADES > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
    Aug-04 09:58:28.779 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 14; name: VIROPROFILER:SPADES (UC20); status: COMPLETED; exit: 0; error: -; workDir: /root/work/97/33a164a105b2f671c0fa220bf78e11]
    Aug-04 09:58:28.783 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:SPADES > Skipping output binding because one or more optional files are missing: fileoutparam<2:1>
    Aug-04 09:58:28.783 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Process VIROPROFILER:SPADES > Skipping output binding because one or more optional files are missing: fileoutparam<3:1>
    Aug-04 09:58:28.805 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:58:28.805 [Task submitter] INFO nextflow.Session - [03/e1d758] Submitted process > VIROPROFILER:CONTIGLIB
    Aug-04 09:58:30.180 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 16; name: VIROPROFILER:CONTIGLIB; status: COMPLETED; exit: 0; error: -; workDir: /root/work/03/e1d75880db1d21fbc119acfca0298e]
    Aug-04 09:58:30.203 [Actor Thread 2] DEBUG nextflow.util.CacheHelper - Hash asset file sha-256: /root/.nextflow/assets/deng-lab/viroprofiler/bin/run_checkv.sh
    Aug-04 09:58:30.211 [Task submitter] DEBUG n.executor.local.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
    Aug-04 09:58:30.211 [Task submitter] INFO nextflow.Session - [ec/257e6e] Submitted process > VIROPROFILER:CHECKV
    Aug-04 10:00:08.228 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 17; name: VIROPROFILER:CHECKV; status: COMPLETED; exit: 1; error: -; workDir: /root/work/ec/257e6e3b81260568daf2a6d5051fb4]
    Aug-04 10:00:08.230 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
    task: name=VIROPROFILER:CHECKV; work-dir=/root/work/ec/257e6e3b81260568daf2a6d5051fb4
    error [nextflow.exception.ProcessFailedException]: Process VIROPROFILER:CHECKV terminated with an error exit status (1)
    Aug-04 10:00:08.237 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'VIROPROFILER:CHECKV'

Caused by:
Process VIROPROFILER:CHECKV terminated with an error exit status (1)

Command executed:

run_checkv.sh contigs_cclib_long.fasta.gz 3000 $(pwd) 1 spades /root/viroprofiler/checkv
mv viruses.fna checkv_qc.fasta
while [ -s proviruses_nextInput.fna ] ; do
dir_new=run_$(date +"%Y%m%d%h%s")
run_checkv.sh proviruses_nextInput.fna 3000 $dir_new 1 spades /root/viroprofiler/checkv
cat $dir_new/viruses.fna >> checkv_qc.fasta
csvtk concat -t quality_summary_viruses.tsv $dir_new/quality_summary_viruses.tsv > quality_summary.tsv
cp quality_summary.tsv quality_summary_viruses.tsv
sed 1d $dir_new/quality_summary_proviruses.tsv >> quality_summary_proviruses.tsv
cat $dir_new/proviruses_short.fna >> proviruses_short.fna
cat $dir_new/proviruse_ids_raw.list >> proviruse_ids_raw.list
cat $dir_new/proviruse_ids_clean.list >> proviruse_ids_clean.list
cp $dir_new/proviruses_nextInput.fna .
sleep 1
done
seqkit seq -m 3000 checkv_qc.fasta > checkv_qc_long.fasta

cat <<-END_VERSIONS > versions.yml
"VIROPROFILER:CHECKV":
CheckV: $(echo $(checkv | head -n1 | sed 's/:.*//' | sed 's/CheckV v//'))
END_VERSIONS

Command exit status:
1

Command output:
(empty)

Command error:

CheckV v1.0.1: contamination
[1/8] Reading database info...
[2/8] Reading genome info...
[3/8] Calling genes with Prodigal...
[4/8] Reading gene info...
[5/8] Running hmmsearch...
[6/8] Annotating genes...
[7/8] Identifying host regions...
[8/8] Writing results...
Run time: 73.23 seconds
Peak mem: 0.24 GB

CheckV v1.0.1: completeness
[1/8] Skipping gene calling...
[2/8] Initializing queries and database...
[3/8] Running DIAMOND blastp search...
[4/8] Computing AAI...
[5/8] Running AAI based completeness estimation...
[6/8] Running HMM based completeness estimation...
[7/8] Determining genome copy number...
[8/8] Writing results...
Run time: 23.19 seconds
Peak mem: 1.92 GB

CheckV v1.0.1: complete_genomes
[1/7] Reading input sequences...
[2/7] Finding complete proviruses...
[3/7] Finding direct/inverted terminal repeats...
[4/7] Filtering terminal repeats...
[5/7] Checking genome for completeness...
[6/7] Checking genome for large duplications...
[7/7] Writing results...
Run time: 0.02 seconds
Peak mem: 1.92 GB

CheckV v1.0.1: quality_summary
[1/6] Reading input sequences...
[2/6] Reading results from contamination module...
[3/6] Reading results from completeness module...
[4/6] Reading results from complete genomes module...
[5/6] Classifying contigs into quality tiers...
[6/6] Writing results...
Run time: 0.01 seconds
Peak mem: 1.92 GB
Traceback (most recent call last):
File "/root/.nextflow/assets/deng-lab/viroprofiler/bin/correct_spades_contig_length.py", line 5, in
from Bio import SeqIO
ModuleNotFoundError: No module named 'Bio'

Work dir:
/root/work/ec/257e6e3b81260568daf2a6d5051fb4

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh
Aug-04 10:00:08.241 [Task monitor] INFO nextflow.Session - Execution cancelled -- Finishing pending tasks before exit
Aug-04 10:00:08.246 [main] DEBUG nextflow.Session - Session await > all processes finished
Aug-04 10:00:08.246 [main] DEBUG nextflow.Session - Session await > all barriers passed
Aug-04 10:00:08.249 [Actor Thread 12] DEBUG nextflow.sort.BigSort - Sort completed -- entries: 4; slices: 1; internal sort time: 0.003 s; external sort time: 0.001 s; total time: 0.004 s
Aug-04 10:00:08.252 [Actor Thread 12] DEBUG nextflow.file.FileCollector - Saved collect-files list to: /root/work/collect-file/7ccdbcda8a5a638859c958f166ae11db
Aug-04 10:00:08.253 [Actor Thread 12] DEBUG nextflow.file.FileCollector - Deleting file collector temp dir: /tmp/nxf-5278134370414411846
Aug-04 10:00:08.256 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'PublishDir' shutdown completed (hard=false)
Aug-04 10:00:08.257 [main] INFO nextflow.Nextflow - -�[0;35m[ViroProfiler]�[0;31m Pipeline completed with errors�[0m-
Aug-04 10:00:08.260 [main] DEBUG nextflow.trace.WorkflowStatsObserver - Workflow completed > WorkflowStats[succeededCount=16; failedCount=1; ignoredCount=0; cachedCount=0; pendingCount=0; submittedCount=0; runningCount=0; retriesCount=0; abortedCount=0; succeedDuration=3m 2s; failedDuration=1m 38s; cachedDuration=0ms;loadCpus=0; loadMemory=0; peakRunning=7; peakCpus=7; peakMemory=14 GB; ]
Aug-04 10:00:08.260 [main] DEBUG nextflow.trace.TraceFileObserver - Workflow completed -- saving trace file
Aug-04 10:00:08.261 [main] DEBUG nextflow.trace.ReportObserver - Workflow completed -- rendering execution report
Aug-04 10:00:08.290 [main] DEBUG nextflow.trace.ReportObserver - Execution report summary data:
[{"cpuUsage":{"mean":129.3,"min":112.1,"q1":113.3,"q2":117.1,"q3":132.8,"max":171.2,"minLabel":"VIROPROFILER:FASTQC (UC21)","maxLabel":"VIROPROFILER:FASTQC (UC24)","q1Label":"VIROPROFILER:FASTQC (UC20)","q2Label":"VIROPROFILER:FASTQC (HT04)","q3Label":"VIROPROFILER:FASTQC (HT02)"},"process":"FASTQC","mem":{"mean":286574182.4,"min":239505408,"q1":261390336,"q2":291016704,"q3":308551680,"max":332406784,"minLabel":"VIROPROFILER:FASTQC (HT02)","maxLabel":"VIROPROFILER:FASTQC (HT04)","q1Label":"VIROPROFILER:FASTQC (UC24)","q2Label":"VIROPROFILER:FASTQC (UC21)","q3Label":"VIROPROFILER:FASTQC (UC20)"},"memUsage":{"mean":13.34,"min":11.15,"q1":12.17,"q2":13.55,"q3":14.37,"max":15.48,"minLabel":"VIROPROFILER:FASTQC (HT02)","maxLabel":"VIROPROFILER:FASTQC (HT04)","q1Label":"VIROPROFILER:FASTQC (UC24)","q2Label":"VIROPROFILER:FASTQC (UC21)","q3Label":"VIROPROFILER:FASTQC (UC20)"},"timeUsage":{"mean":0.01,"min":0.01,"q1":0.01,"q2":0.01,"q3":0.02,"max":0.02,"minLabel":"VIROPROFILER:FASTQC (UC24)","maxLabel":"VIROPROFILER:FASTQC (UC20)","q1Label":"VIROPROFILER:FASTQC (HT02)","q2Label":"VIROPROFILER:FASTQC (UC21)","q3Label":"VIROPROFILER:FASTQC (HT04)"},"vmem":{"mean":3303808204.8,"min":3283750912,"q1":3284742144,"q2":3307405312,"q3":3307405312,"max":3335737344,"minLabel":"VIROPROFILER:FASTQC (UC20)","maxLabel":"VIROPROFILER:FASTQC (UC21)","q1Label":"VIROPROFILER:FASTQC (HT04)","q2Label":"VIROPROFILER:FASTQC (HT02)","q3Label":"VIROPROFILER:FASTQC (UC24)"},"reads":{"mean":23803429.4,"min":22835380,"q1":23135026,"q2":23560292,"q3":24362904,"max":25123545,"minLabel":"VIROPROFILER:FASTQC (HT02)","maxLabel":"VIROPROFILER:FASTQC (HT04)","q1Label":"VIROPROFILER:FASTQC (UC21)","q2Label":"VIROPROFILER:FASTQC (UC24)","q3Label":"VIROPROFILER:FASTQC (UC20)"},"cpu":{"mean":129.3,"min":112.1,"q1":113.3,"q2":117.1,"q3":132.8,"max":171.2,"minLabel":"VIROPROFILER:FASTQC (UC21)","maxLabel":"VIROPROFILER:FASTQC (UC24)","q1Label":"VIROPROFILER:FASTQC (UC20)","q2Label":"VIROPROFILER:FASTQC (HT04)","q3Label":"VIROPROFILER:FASTQC (HT02)"},"time":{"mean":6200,"min":5000,"q1":6000,"q2":6000,"q3":7000,"max":7000,"minLabel":"VIROPROFILER:FASTQC (UC24)","maxLabel":"VIROPROFILER:FASTQC (UC20)","q1Label":"VIROPROFILER:FASTQC (HT02)","q2Label":"VIROPROFILER:FASTQC (UC21)","q3Label":"VIROPROFILER:FASTQC (HT04)"},"writes":{"mean":3906933.6,"min":3867657,"q1":3895060,"q2":3895592,"q3":3931918,"max":3944441,"minLabel":"VIROPROFILER:FASTQC (HT04)","maxLabel":"VIROPROFILER:FASTQC (HT02)","q1Label":"VIROPROFILER:FASTQC (UC24)","q2Label":"VIROPROFILER:FASTQC (UC20)","q3Label":"VIROPROFILER:FASTQC (UC21)"}},{"cpuUsage":{"mean":98.14,"min":91.8,"q1":98.1,"q2":99.4,"q3":100.4,"max":101,"minLabel":"VIROPROFILER:FASTP (HT02)","maxLabel":"VIROPROFILER:FASTP (UC24)","q1Label":"VIROPROFILER:FASTP (UC20)","q2Label":"VIROPROFILER:FASTP (HT04)","q3Label":"VIROPROFILER:FASTP (UC21)"},"process":"FASTP","mem":{"mean":840258355.2,"min":222191616,"q1":250228736,"q2":1201082368,"q3":1229742080,"max":1298046976,"minLabel":"VIROPROFILER:FASTP (UC20)","maxLabel":"VIROPROFILER:FASTP (UC24)","q1Label":"VIROPROFILER:FASTP (HT04)","q2Label":"VIROPROFILER:FASTP (HT02)","q3Label":"VIROPROFILER:FASTP (UC21)"},"memUsage":{"mean":39.13,"min":10.35,"q1":11.65,"q2":55.93,"q3":57.26,"max":60.45,"minLabel":"VIROPROFILER:FASTP (UC20)","maxLabel":"VIROPROFILER:FASTP (UC24)","q1Label":"VIROPROFILER:FASTP (HT04)","q2Label":"VIROPROFILER:FASTP (HT02)","q3Label":"VIROPROFILER:FASTP (UC21)"},"timeUsage":{"mean":0.02,"min":0.02,"q1":0.02,"q2":0.03,"q3":0.03,"max":0.03,"minLabel":"VIROPROFILER:FASTP (UC21)","maxLabel":"VIROPROFILER:FASTP (HT04)","q1Label":"VIROPROFILER:FASTP (HT02)","q2Label":"VIROPROFILER:FASTP (UC24)","q3Label":"VIROPROFILER:FASTP (UC20)"},"vmem":{"mean":1009523097.6,"min":227385344,"q1":255365120,"q2":1437638656,"q3":1531510784,"max":1595715584,"minLabel":"VIROPROFILER:FASTP (UC20)","maxLabel":"VIROPROFILER:FASTP (UC24)","q1Label":"VIROPROFILER:FASTP (HT04)","q2Label":"VIROPROFILER:FASTP (HT02)","q3Label":"VIROPROFILER:FASTP (UC21)"},"reads":{"mean":7784934.4,"min":3802474,"q1":5021920,"q2":6914059,"q3":10124558,"max":13061661,"minLabel":"VIROPROFILER:FASTP (HT02)","maxLabel":"VIROPROFILER:FASTP (HT04)","q1Label":"VIROPROFILER:FASTP (UC21)","q2Label":"VIROPROFILER:FASTP (UC24)","q3Label":"VIROPROFILER:FASTP (UC20)"},"cpu":{"mean":98.14,"min":91.8,"q1":98.1,"q2":99.4,"q3":100.4,"max":101,"minLabel":"VIROPROFILER:FASTP (HT02)","maxLabel":"VIROPROFILER:FASTP (UC24)","q1Label":"VIROPROFILER:FASTP (UC20)","q2Label":"VIROPROFILER:FASTP (HT04)","q3Label":"VIROPROFILER:FASTP (UC21)"},"time":{"mean":10600,"min":7000,"q1":8000,"q2":11000,"q3":13000,"max":14000,"minLabel":"VIROPROFILER:FASTP (UC21)","maxLabel":"VIROPROFILER:FASTP (HT04)","q1Label":"VIROPROFILER:FASTP (HT02)","q2Label":"VIROPROFILER:FASTP (UC24)","q3Label":"VIROPROFILER:FASTP (UC20)"},"writes":{"mean":2458686.4,"min":1480500,"q1":1781994,"q2":2246320,"q3":3032593,"max":3752025,"minLabel":"VIROPROFILER:FASTP (HT02)","maxLabel":"VIROPROFILER:FASTP (HT04)","q1Label":"VIROPROFILER:FASTP (UC21)","q2Label":"VIROPROFILER:FASTP (UC24)","q3Label":"VIROPROFILER:FASTP (UC20)"}},{"cpuUsage":{"mean":102.38,"min":100.4,"q1":101.5,"q2":102.3,"q3":103.8,"max":103.9,"minLabel":"VIROPROFILER:SPADES (UC20)","maxLabel":"VIROPROFILER:SPADES (UC21)","q1Label":"VIROPROFILER:SPADES (HT04)","q2Label":"VIROPROFILER:SPADES (UC24)","q3Label":"VIROPROFILER:SPADES (HT02)"},"process":"SPADES","mem":{"mean":91026227.2,"min":67903488,"q1":79626240,"q2":81346560,"q3":108244992,"max":118009856,"minLabel":"VIROPROFILER:SPADES (UC21)","maxLabel":"VIROPROFILER:SPADES (HT04)","q1Label":"VIROPROFILER:SPADES (UC20)","q2Label":"VIROPROFILER:SPADES (HT02)","q3Label":"VIROPROFILER:SPADES (UC24)"},"memUsage":{"mean":1.41,"min":1.05,"q1":1.24,"q2":1.26,"q3":1.68,"max":1.83,"minLabel":"VIROPROFILER:SPADES (UC21)","maxLabel":"VIROPROFILER:SPADES (HT04)","q1Label":"VIROPROFILER:SPADES (UC20)","q2Label":"VIROPROFILER:SPADES (HT02)","q3Label":"VIROPROFILER:SPADES (UC24)"},"timeUsage":{"mean":0.02,"min":0.01,"q1":0.01,"q2":0.01,"q3":0.02,"max":0.06,"minLabel":"VIROPROFILER:SPADES (HT02)","maxLabel":"VIROPROFILER:SPADES (UC20)","q1Label":"VIROPROFILER:SPADES (UC21)","q2Label":"VIROPROFILER:SPADES (UC24)","q3Label":"VIROPROFILER:SPADES (HT04)"},"vmem":{"mean":907386880,"min":907386880,"q1":907386880,"q2":907386880,"q3":907386880,"max":907386880,"minLabel":"VIROPROFILER:SPADES (HT02)","maxLabel":"VIROPROFILER:SPADES (UC20)","q1Label":"VIROPROFILER:SPADES (UC21)","q2Label":"VIROPROFILER:SPADES (HT04)","q3Label":"VIROPROFILER:SPADES (UC24)"},"reads":{"mean":69519339,"min":42067857,"q1":50567248,"q2":68099897,"q3":76635121,"max":110226572,"minLabel":"VIROPROFILER:SPADES (HT02)","maxLabel":"VIROPROFILER:SPADES (HT04)","q1Label":"VIROPROFILER:SPADES (UC21)","q2Label":"VIROPROFILER:SPADES (UC24)","q3Label":"VIROPROFILER:SPADES (UC20)"},"cpu":{"mean":102.38,"min":100.4,"q1":101.5,"q2":102.3,"q3":103.8,"max":103.9,"minLabel":"VIROPROFILER:SPADES (UC20)","maxLabel":"VIROPROFILER:SPADES (UC21)","q1Label":"VIROPROFILER:SPADES (HT04)","q2Label":"VIROPROFILER:SPADES (UC24)","q3Label":"VIROPROFILER:SPADES (HT02)"},"time":{"mean":19400,"min":6000,"q1":7000,"q2":10000,"q3":20000,"max":54000,"minLabel":"VIROPROFILER:SPADES (HT02)","maxLabel":"VIROPROFILER:SPADES (UC20)","q1Label":"VIROPROFILER:SPADES (UC21)","q2Label":"VIROPROFILER:SPADES (UC24)","q3Label":"VIROPROFILER:SPADES (HT04)"},"writes":{"mean":93099341.2,"min":46013225,"q1":61701424,"q2":94467898,"q3":111262918,"max":152051241,"minLabel":"VIROPROFILER:SPADES (HT02)","maxLabel":"VIROPROFILER:SPADES (HT04)","q1Label":"VIROPROFILER:SPADES (UC21)","q2Label":"VIROPROFILER:SPADES (UC24)","q3Label":"VIROPROFILER:SPADES (UC20)"}},{"cpuUsage":{"mean":118.9,"min":118.9,"q1":118.9,"q2":118.9,"q3":118.9,"max":118.9,"minLabel":"VIROPROFILER:CONTIGLIB","maxLabel":"VIROPROFILER:CONTIGLIB","q1Label":"VIROPROFILER:CONTIGLIB","q2Label":"VIROPROFILER:CONTIGLIB","q3Label":"VIROPROFILER:CONTIGLIB"},"process":"CONTIGLIB","mem":{"mean":19066880,"min":19066880,"q1":19066880,"q2":19066880,"q3":19066880,"max":19066880,"minLabel":"VIROPROFILER:CONTIGLIB","maxLabel":"VIROPROFILER:CONTIGLIB","q1Label":"VIROPROFILER:CONTIGLIB","q2Label":"VIROPROFILER:CONTIGLIB","q3Label":"VIROPROFILER:CONTIGLIB"},"memUsage":{"mean":0.44,"min":0.44,"q1":0.44,"q2":0.44,"q3":0.44,"max":0.44,"minLabel":"VIROPROFILER:CONTIGLIB","maxLabel":"VIROPROFILER:CONTIGLIB","q1Label":"VIROPROFILER:CONTIGLIB","q2Label":"VIROPROFILER:CONTIGLIB","q3Label":"VIROPROFILER:CONTIGLIB"},"timeUsage":null,"vmem":{"mean":751820800,"min":751820800,"q1":751820800,"q2":751820800,"q3":751820800,"max":751820800,"minLabel":"VIROPROFILER:CONTIGLIB","maxLabel":"VIROPROFILER:CONTIGLIB","q1Label":"VIROPROFILER:CONTIGLIB","q2Label":"VIROPROFILER:CONTIGLIB","q3Label":"VIROPROFILER:CONTIGLIB"},"reads":{"mean":6201421,"min":6201421,"q1":6201421,"q2":6201421,"q3":6201421,"max":6201421,"minLabel":"VIROPROFILER:CONTIGLIB","maxLabel":"VIROPROFILER:CONTIGLIB","q1Label":"VIROPROFILER:CONTIGLIB","q2Label":"VIROPROFILER:CONTIGLIB","q3Label":"VIROPROFILER:CONTIGLIB"},"cpu":{"mean":118.9,"min":118.9,"q1":118.9,"q2":118.9,"q3":118.9,"max":118.9,"minLabel":"VIROPROFILER:CONTIGLIB","maxLabel":"VIROPROFILER:CONTIGLIB","q1Label":"VIROPROFILER:CONTIGLIB","q2Label":"VIROPROFILER:CONTIGLIB","q3Label":"VIROPROFILER:CONTIGLIB"},"time":{"mean":553,"min":553,"q1":553,"q2":553,"q3":553,"max":553,"minLabel":"VIROPROFILER:CONTIGLIB","maxLabel":"VIROPROFILER:CONTIGLIB","q1Label":"VIROPROFILER:CONTIGLIB","q2Label":"VIROPROFILER:CONTIGLIB","q3Label":"VIROPROFILER:CONTIGLIB"},"writes":{"mean":5240412,"min":5240412,"q1":5240412,"q2":5240412,"q3":5240412,"max":5240412,"minLabel":"VIROPROFILER:CONTIGLIB","maxLabel":"VIROPROFILER:CONTIGLIB","q1Label":"VIROPROFILER:CONTIGLIB","q2Label":"VIROPROFILER:CONTIGLIB","q3Label":"VIROPROFILER:CONTIGLIB"}},{"cpuUsage":null,"process":"CHECKV","mem":null,"memUsage":null,"timeUsage":{"mean":0.23,"min":0.23,"q1":0.23,"q2":0.23,"q3":0.23,"max":0.23,"minLabel":"VIROPROFILER:CHECKV","maxLabel":"VIROPROFILER:CHECKV","q1Label":"VIROPROFILER:CHECKV","q2Label":"VIROPROFILER:CHECKV","q3Label":"VIROPROFILER:CHECKV"},"vmem":null,"reads":null,"cpu":null,"time":{"mean":97947,"min":97947,"q1":97947,"q2":97947,"q3":97947,"max":97947,"minLabel":"VIROPROFILER:CHECKV","maxLabel":"VIROPROFILER:CHECKV","q1Label":"VIROPROFILER:CHECKV","q2Label":"VIROPROFILER:CHECKV","q3Label":"VIROPROFILER:CHECKV"},"writes":null}]
Aug-04 10:00:08.628 [main] DEBUG nextflow.trace.TimelineObserver - Workflow completed -- rendering execution timeline
Aug-04 10:00:08.849 [main] DEBUG nextflow.cache.CacheDB - Closing CacheDB done
Aug-04 10:00:08.857 [main] DEBUG nextflow.util.ThreadPoolManager - Thread pool 'FileTransfer' shutdown completed (hard=false)
Aug-04 10:00:08.858 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye

System information

nextflow version 23.04.2.5870
ubuntu 22.04
@flowhub-team flowhub-team added the bug Something isn't working label Aug 4, 2023
@kaanb93 kaanb93 mentioned this issue Aug 11, 2023
Open
@rujinlong
Copy link
Collaborator

Hi @flowhub-team. This issue arises from the multi-env in micromamba (refer to nextflow-io/nextflow#3206). It seems that your Docker didn't activate the correct conda environment. However, I can't reproduce this error. Could you please update Docker to the latest version and try again? If the problem persists, you have two other options:

  1. Use Singularity instead of Docker.
  2. In the next release (scheduled for the end of this month), I will separate the multi-env into different container images, so that each image contains only one base environment.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@rujinlong @flowhub-team